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comparison cuffdiff_wrapper.py @ 13:4597c429b6fb

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Return nonzero exit code from cuffdiff_wrapper.py on error
author Jim Johnson <jj@umn.edu>
date Wed, 17 Jul 2013 07:58:39 -0500
parents 6a9bc26ab8d9
children d10befb0867a
comparison
equal deleted inserted replaced
12:e132e60f95b1 13:4597c429b6fb
31 31
32 setattr(parser.values, option.dest, labels) 32 setattr(parser.values, option.dest, labels)
33 33
34 def stop_err( msg ): 34 def stop_err( msg ):
35 sys.stderr.write( "%s\n" % msg ) 35 sys.stderr.write( "%s\n" % msg )
36 sys.exit() 36 sys.exit(1)
37 37
38 # Copied from sam_to_bam.py: 38 # Copied from sam_to_bam.py:
39 def check_seq_file( dbkey, cached_seqs_pointer_file ): 39 def check_seq_file( dbkey, cached_seqs_pointer_file ):
40 seq_path = '' 40 seq_path = ''
41 for line in open( cached_seqs_pointer_file ): 41 for line in open( cached_seqs_pointer_file ):